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Related Concept Videos

Protein Folding01:22

Protein Folding

Overview
Protein Folding01:25

Protein Folding

Proteins are chains of amino acids linked together by peptide bonds. Upon synthesis, a protein folds into a three-dimensional conformation, critical to its biological function. Interactions between its constituent amino acids guide protein folding, and hence the protein structure is primarily dependent on its amino acid sequence.
Protein Structure Is Critical to Its Biological Function
Proteins perform a wide range of biological functions such as catalyzing chemical reactions, providing...
Protein and Protein Structure02:15

Protein and Protein Structure

Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective. They may serve in transport, storage, or membranes; or they may be toxins or enzymes. Their structures, like their functions, vary greatly. They are all, however, amino acid polymers arranged in a linear sequence.
A protein's shape is critical to its function. For example, an enzyme can...
X-ray Diffraction of Biological Samples01:10

X-ray Diffraction of Biological Samples

X-ray diffraction or XRD is an analytical tool that utilizes X-rays to study ordered structures such as crystalline organic and inorganic samples, polycrystalline materials, proteins, carbohydrates, and drugs.
According to Bragg's law, when X-rays strike the sample positioned on a stage, the rays are  scattered by the electron clouds around the sample atoms. The  X-ray diffraction or scattering is caused by constructive interference of the X-ray waves that reflect off the internal crystal...
Intrinsically Disordered Proteins02:18

Intrinsically Disordered Proteins

Intrinsically disordered proteins are a group of proteins that do not fold into specific three-dimensional structures. Their structural flexibility allows them to complement ordered proteins to perform functions that are inaccessible to rigid structures. They are more common in eukaryotes than prokaryotes and may either be exclusively intrinsically disordered or hybrid proteins, consisting of a mix of ordered and disordered regions. The absence of a rigid structure in these proteins can be...
Protein Organization01:24

Protein Organization

Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence.

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Structural Studies of Macromolecules in Solution using Small Angle X-Ray Scattering
07:19

Structural Studies of Macromolecules in Solution using Small Angle X-Ray Scattering

Published on: November 5, 2018

Structure and flexibility within proteins as identified through small angle X-ray scattering.

Martin Pelikan1, Greg L Hura, Michal Hammel

  • 1Department of Mathematics and Computer Science, University of Missouri in St. Louis, St. Louis, Missouri 63121, USA.

General Physiology and Biophysics
|July 14, 2009
PubMed
Summary

Small angle X-ray scattering (SAXS) and computational modeling identify protein flexibility. This approach validates minimal ensembles representing protein conformations in solution, aiding structural analysis.

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Time-Resolved Fluorescence Anisotropy from Single Molecules for Characterizing Local Flexibility in Biomolecules

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Area of Science:

  • Structural Biology
  • Biophysics
  • Computational Biology

Background:

  • Protein flexibility is crucial for biological function but challenging to study with conventional methods like X-ray crystallography or NMR.
  • Understanding protein domain motions in solution is essential for elucidating mechanisms of action.
  • Postulating flexibility sites after high-resolution structure determination is a common but often insufficient approach.

Purpose of the Study:

  • To present a novel analysis tool combining small angle X-ray scattering (SAXS) and computational modeling to identify and characterize protein flexibility.
  • To validate a minimal ensemble of models representing the most populated protein conformations in solution.
  • To determine the types of conformations protein domains sample in solution.

Main Methods:

  • Utilized inexpensive small angle X-ray scattering (SAXS) measurements for solution-based structural analysis.
  • Employed rigid body modeling with BILBOMD and molecular dynamics (MD) simulations to explore protein conformational space.
  • Applied a genetic algorithm for minimal ensemble search (MES) to identify the smallest set of models fitting experimental SAXS data.

Main Results:

  • The developed SAXS-based method successfully identified protein flexibility and validated constructed minimal ensembles.
  • The resolution achieved was sufficient to characterize the conformational landscape sampled by protein domains in solution.
  • Demonstrated the utility of MES for analyzing both model systems and four experimental biological examples.

Conclusions:

  • The combination of SAXS and computational modeling provides a powerful approach to study large-scale protein flexibility.
  • The minimal ensemble search (MES) method effectively represents the dynamic nature of proteins in solution.
  • This integrated strategy offers valuable insights into protein conformational ensembles, complementing traditional structural biology techniques.